/*===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
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*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
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*  Please cite the author in any work or product based on this material.
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* ===========================================================================
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*/

#ifndef _h_rna_splice_log_
#define _h_rna_splice_log_

#include <insdc/insdc.h>
#include <align/reference.h>

#ifdef __cplusplus
extern "C" {
#endif


#define INTRON_UNKNOWN 0
#define INTRON_FWD 1
#define INTRON_REV 2

typedef struct splice_dict_entry splice_dict_entry;
struct splice_dict_entry
{
    uint32_t count;
    uint32_t intron_type;
};

struct rna_splice_dict;

struct rna_splice_dict * make_rna_splice_dict( void );

void free_rna_splice_dict( struct rna_splice_dict * dict );

bool rna_splice_dict_get( struct rna_splice_dict * dict,
                          uint32_t pos,
                          uint32_t len,
                          splice_dict_entry * entry );

void rna_splice_dict_set( struct rna_splice_dict * dict,
                          uint32_t pos,
                          uint32_t len,
                          const splice_dict_entry * entry );

/* --------------------------------------------------------------------------- */


struct rna_splice_log;

struct rna_splice_log * make_rna_splice_log( const char * filename,
                                             const char * toolname );

void free_rna_splice_log( struct rna_splice_log * sl );

void rna_splice_log_enter_ref( struct rna_splice_log * sl,
                               const char * ref_name,
                               struct ReferenceObj const * ref_obj );

void rna_splice_log_exit_ref( struct rna_splice_log * sl,
                              struct rna_splice_dict * dict );


#ifdef __cplusplus
}
#endif

#endif /*  _h_rna_splice_log_ */
